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[R-pkg-devel] Package can't be imported with Suggests

Gaurav Sood

Wed, Aug 5, 2020 3:45 PM

I think the key line = " Unfortunately, nimble will not work with this
mechanism. "

Given that, depends seems like a good short-term solution. Change it to
suggests once the upstream problem is fixed.

On Wed, Aug 5, 2020 at 3:36 PM Simon Bonner <simon.bonner at uwo.ca> wrote:

Hi all,

I?m wondering if someone an offer advice on a problem I?m facing in
developing a package.

My package essentially generates code and formats data for one of two MCMC
sampling engines, JAGS accessed via rjags or nimble (a native R package),
calls the engines, and then provides functions to access the results. Since
only one of the engines is needed I would like to include rjags and nimble
in Suggests in the DESCRIPTION and use requireNamespace() to load the
appropriate package when its functionality is needed.

Unfortunately, nimble will not work with this mechanism. It relies on a
complex mechanism to compile C++ code to run the sampler, and some of the
functions cannot be found when the package is loaded in this way. I?ve been
in touch with the maintainers and they are aware of the issue but the
current fix is to include the package under Depends. However, this forces a
user to install nimble (which itself requires compiling lengthy C++ code)
even if the user intends to run the sampler in JAGS.

I thought I?d solved the problem by including nimble in Suggests and then
loading it via library() so that all of its functions are attached. This
works, but produces a note during the check:
? checking dependencies in R code ... NOTE
  'library' or 'require' call to ?nimble? in package code.
    Please use :: or requireNamespace() instead.
    See section 'Suggested packages' in the 'Writing R Extensions' manual

What is the recommendation?

I see two options:


  1.  Include nimble in Depends and force user to install it.
  2.  Ignore the note and explain the problem when I resubmit to CRAN.

Am I missing anything?

Thanks in advance!

Simon





Simon Bonner
Assistant Professor of Environmetrics
Department of Statistical and Actuarial Sciences
University of Western Ontario

Office: Western Science Centre rm 276

Email: sbonner6 at uwo.ca<mailto:sbonner6 at uwo.ca> | Telephone: 519-661-2111
x88205 | Fax: 519-661-3813
Twitter: @bonnerstatslab | Website:
http://simon.bonners.ca/bonner-lab/wpblog/


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Thread (6 messages)

Simon Bonner Package can't be imported with Suggests Aug 5 Gaurav Sood Package can't be imported with Suggests Aug 5 William Dunlap Package can't be imported with Suggests Aug 5 Dirk Eddelbuettel Package can't be imported with Suggests Aug 5 Jens Oehlschlägel Package can't be imported with Suggests Aug 6 Simon Bonner Package can't be imported with Suggests Aug 7